Re: [Jmol-users] Write 2 PDB models?

Hi Eric I agree it's a bug. I wuld xpect -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most

Re: [Jmol-users] Write 2 PDB models?

Hi Eric I agree it's a bug. I would expect both models to be saved, and the doc says "Only the currently selected atoms are saved." If you save to SDF it works as expected. The fact that the file has MODEL ENDMDL means that Jmol is indeed intending to save both. So for proteins, you could

[Jmol-users] Write 2 PDB models?

If I load 2 models, then "frame all; select all;", I expect that "write PDB" will write both models. Instead, the PDB file has MODEL/ENDMDL records for 2 models, but the first model contains no coordinates. Is this a bug or a feature? load =3hyd load append =4qxx frame all select all write

Re: [Jmol-users] JSME and SMILES

Bob, I realize that Jmol uses Ajax. So I’ve been using Ajax all along. This was my first time I wrote the Ajax HTML and JavaScript myself to communicate with server-side PHP code I also wrote myself. So it felt different to me. Jennifer Jennifer Muzyka H.W. Stodghill Jr. and Adele H.

Re: [Jmol-users] JSME and SMILES

Here’s the documentation that served as the reading for the fall 2015 OLCC course on cheminformatics, from http://olcc.ccce.divched.org/2015OLCCModule5P1#3.2 Because the layered structure of InChI allows one to represent a chemical structure with a desired level of details, InChI software may

Re: [Jmol-users] JSME and SMILES

On Fri, Jul 22, 2016 at 8:42 AM, Jennifer L. Muzyka < jennifer.muz...@centre.edu> wrote: > InChI is very messy because there’s more than one version of the program > that generates it. So depending on what version you use, you get a > different InChI. That information about which version of the

Re: [Jmol-users] JSME and SMILES

InChI is very messy because there’s more than one version of the program that generates it. So depending on what version you use, you get a different InChI. That information about which version of the InChI rules you are using is an early part of the string. The other problem with InChI is

Re: [Jmol-users] JSME and SMILES

Bob, I was under the impression that canonical SMILES would be the same from one program to another, not just from the same program. I participated in the Fall 2015 OLCC on cheminformatics, and that’s what I remember us teaching the students. So the distinction you are making is reasonable to

Re: [Jmol-users] Rapamycin

Great idea, Angel. load ==RAP ​ -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth.

Re: [Jmol-users] JSME and SMILES

Hi, Jennifer. "Canonical" SMILES just means that a given version of a given program will always report out the same string for a compound. Key words there are "same program" and "same version". So if you used an earlier version of a program to create a database of strings to compare, then you